Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,434,882	0	T	G	50.0%	67.2 / 12.9	50	Y252S (TAC→TCC)	truA	tRNA pseudouridine(38‑40) synthase
Reads supporting (aligned to +/- strand):  ref base T (6/19);  new base G (25/0);  total (31/19)
Fisher's exact test for biased strand distribution p-value = 1.16e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACA‑GCCCTTCCGCTTTTGCCGTTGCTG‑CCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTG  >  NC_000913/2434736‑2435025                                                                                                                                                   |                                                                                                                                                  gTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATACCGGGCCGGGGaa                                                                                                                                                 >  1:288847/1‑149 (MQ=255)          tGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGCATGGCACACCGGTCCCGGTGATCCAcccc                                                                                                                                         >  1:548385/1‑146 (MQ=255)           gCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGGTTTTGTAGAGGATAACGGTGAGGGGaacacac                                                                                                                                            >  1:205724/1‑139 (MQ=255)             cTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATCATTCCGGGCAGGGTAATCCACCGCGGcc                                                                                                                                     >  1:6426/1‑149 (MQ=255)                     tGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACA‑Gc                                                                                                                           <  2:454102/150‑1 (MQ=255)                        aCTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACA‑GCCCtt                                                                                                                       <  1:173382/151‑1 (MQ=255)                             tCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACA‑GCCCTTcc                                                                                                                     <  1:292305/148‑1 (MQ=255)                              cATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACA‑GCCCTTCCGCt                                                                                                                  <  1:289486/150‑1 (MQ=255)                                tCTTTCAGGCTGTAACTACGTTGGCTACCGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGAACATACCCGGCAGGGGAATCAACCCCGACCAGATACA‑GACCTTTCCCtttt                                                                                                               >  1:542950/1‑151 (MQ=255)                                   ttCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGGAGATCATACCCGTCAGGGGAATCCACCGCGACCAGATACA‑GCCCCTCCGCCTTTTcc                                                                                                            >  2:630974/1‑151 (MQ=255)                                   ttCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCCGTCCGGGGAAACCACCGCGACCACATACA‑GCCCCTCCGCcttt                                                                                                               >  2:254958/1‑148 (MQ=255)                                       ggCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCCGTCAGGGGAAACATCCCCGACCAGAAACA‑ACCCTTCCGCTTTTGCCGtt                                                                                                         >  2:484531/1‑150 (MQ=255)                                          tGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATCATACCGGTCAGGGGAATCCACCGCGACCAGATACA‑ACCCCTCCGCTTTTTCCGtt                                                                                                         >  2:2448/1‑147 (MQ=255)                                                 aCGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACA‑GCCCTTCCGCTTTTGCCGTTGCTG‑CCGCCa                                                                                              <  2:354363/150‑1 (MQ=255)                                                  cGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAACAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCCGGCAGGGGAATCCACCGCGACCAGATACA‑GCCCCTCCGCTTTTTCCGTTGCTg‑ccccc                                                                                               >  2:456622/1‑148 (MQ=255)                                                     tGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACA‑GCCCTTCCGCTTTTGCCGTTGCTG‑CCGCCAGCGt                                                                                          <  1:448525/150‑1 (MQ=255)                                                      ggCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACA‑GCCCTTCCGCTTTTGCCGTTGCTG‑CCGCCAGCGTTc                                                                                        <  2:201685/151‑1 (MQ=255)                                                          aCAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATTATACCCGTCAGGGGAAATCACCCCGACCAGATACA‑ACCCCTCCCCTTTTTCCGTTGCTG‑CCGCCAGc                                                                                            >  1:426376/1‑143 (MQ=255)                                                               cTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAAATCATACCCGGCAGGGGAATCCACCGCGGCCAGATACA‑GCCCCTCCGCTTTTTCCGTTGCTG‑CCGCCCGCGTTTTGTCCttt                                                                                >  2:434383/1‑150 (MQ=255)                                                                tGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGGTTTTGTAGATCATACCCGTCAGGGGAATTCACCCCGGCCAGAAACA‑ACCCTTTCCCTTTTTGCGGTTCTG‑TCCCCAGCGGTTTGTCCttt                                                                                >  1:429864/1‑149 (MQ=255)                                                                      gTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATACCGGGCCGGGGAATCCACCCCGACCCGATAAA‑GCCCCTCCGCCTTTGCCGGTGCTG‑CCCCCCGCGTTCTGTCCTTTttcgccc                                                                         >  1:63490/1‑149 (MQ=255)                                                                        tCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGGAATCCACCGCGACCAGATACA‑GCCCTTCCGCTTTTTCCGTTGCTG‑CCGCCAGCGTTCTGTCCTTTtccgcc                                                                          >  2:447320/1‑147 (MQ=255)                                                                        tCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTCTTGGAAGATCATAACGGGTAGGGGAAACAACCGCGACCAAATACC‑ACCCTTCCGCTTTTTCCGTTGCTGTCCCCCCCCGTT‑TTTCCTTTgccccc                                                                          >  2:581524/1‑147 (MQ=255)                                                                           gAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCAGGCCGGGGAAAACAACGCGGCCAGATAAA‑ACCCTTCCGCTTTTTGCGGTGGTG‑CCGCCCGCGTTCTGTTCTTTCCCGGCAGCaa                                                                     >  2:427754/1‑149 (MQ=255)                                                                             gCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGGAGATCATACCGGTCAGGGGAATCCACCGCGACCAGATACA‑GCCCTTCCGCTTTTGCCGTTGCTG‑CCGCCAGCGTTCTGTCCTTTTCCGCCCGCAActc                                                                  >  2:310109/1‑150 (MQ=255)                                                                               attattCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATTATACCCGGCCGGGGAATCCACCCCGACCAGATACA‑ACCCTTCCTCTTTTTCCGCTGCTG‑CCGCCCGCGGTCTTTCCTTTGCCGCCAGCCActct                                                                 >  2:193569/1‑149 (MQ=255)                                                                                    tctcGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGGAGATCATACCGGGTCGGGGAATCCACCGCGACCCGATACACGCCTTTCCCCTTTT‑CCGGTGCTG‑CCGCCAGCGTTCTGTCCTTTGCCGCCAGCCACCCTTCCATcc                                                          >  1:604482/1‑151 (MQ=255)                                                                                     ctcGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGGAGATCATACCGGGCAGGGGAATCCACCGCGACCAGATACA‑GCCCTTCCGCTTTTTCCGTTTCTG‑CCCCCAGCGCTCTTTTCCTTGCCGCCCGCAACTCTGCttttc                                                          >  1:27612/1‑146 (MQ=255)                                                                                       cGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGGAGATCATAACGGGCCGGGGAAACCACCGCGACCAGATAAA‑ACCCTTCCCCTTTTTCCGTTGCTG‑CCCCCCCCGGTCTGTCCTTTTCCCCCCGCCACTCTTCTATcc                                                          >  1:594783/1‑148 (MQ=255)                                                                                       cGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACA‑GCCCTTCCGCTTTTGCCGTTGCTG‑CCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAg                                                        <  2:252990/150‑1 (MQ=255)                                                                                              ccGCCAGAAATAGCGGGCCCATTGGCGGTTTTTGAAGATACTACCGGTCAGGGGAAACCACCCCGACCAGATACA‑GCCCTTCCGCTTTTGCCGTTGCTG‑CCCCCCGCGTTCTGTCCTTTGCCCCCCGCCACCCTTCTAttcctctc                                                     >  2:240934/1‑139 (MQ=255)                                                                                                 ccAGAAATAGCGGGCCCATT‑GCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACA‑GCCCTTCCGCTTTTGCCGTTGCTG‑CCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTgg                                            >  2:326960/1‑151 (MQ=255)                                                                                                  cAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACA‑GCCCTTCCGCTTTTGCCGTTGCTG‑CCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTgg                                            <  2:697393/151‑1 (MQ=255)                                                                                                  cAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGGAAACCACCGCGACCAGATACA‑ACCCTTCCGCTTTTGCCGTTGCTG‑CCGCCAGCGTTCTGTCCTTTTCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTgg                                            >  2:452461/1‑151 (MQ=255)                                                                                                     aaaTAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACA‑GCCCTTCCGCTTTTGCCGTTGCTG‑CCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTtg                                         <  1:609735/151‑1 (MQ=255)                                                                                                       aTAGCGGGCCCATTGGCGGTTTTTGAAGATCATACCGGTCAGGGGAATCCACCGCGACCAGATAAA‑GCCCTTCCGCTTTTTCCGTTGCTG‑CCGCCAGCGGTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCCGCTCTCCGGCTGGTtgt                                        >  2:647847/1‑150 (MQ=255)                                                                                                       aTAGCGGGCCCATTGGCGGTTTTTGAAGATCATACCGGGCAGGGGAATCCACCCCGACCAGATACA‑ACCCCTCCCCTTTTTCCGTTGCTG‑CCGCCAGCGTTCTGTCCTTTTCCGCCAGCAACTCTGCTATCCCGCTCTCCCGCTgggt                                          >  2:250137/1‑146 (MQ=255)                                                                                                       aTAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACA‑GCCCTTCCGCTTTTGCCGTTGCTG‑CCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTtgtg                                       <  1:191554/151‑1 (MQ=255)                                                                                                           cGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACA‑GCCCTTCCGCTTTTGCCGTTGCTG‑CCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCa                                   <  1:138813/151‑1 (MQ=255)                                                                                                               cccATTGGCGGTTTTGGAAGATCATACCCGGCAGGGGAATCCACCCCGACCCGATACA‑GCCCCTTCGCTCTTGCCGTTGCTG‑CCGCCAGCGTTCTGTCCTTTGTCGCCAGCAACTCTGCTTTCCAGCTCTCCCGCCGGTTGTggggccc                                 >  1:572811/1‑145 (MQ=255)                                                                                                                  aTTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACA‑GCCCTTCCGCTTTTGCCGTTGCTG‑CCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACtt                            <  1:434346/151‑1 (MQ=255)                                                                                                                      gCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACA‑GCCCTTCCGCTTTTGCCGTTGCTG‑CCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCAt                        >  2:156850/1‑151 (MQ=255)                                                                                                                      gCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACA‑GCCCTTCCGCTTTTGCCGTTGCTG‑CCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCAt                        <  2:397619/151‑1 (MQ=255)                                                                                                                       cGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACA‑GCCCTTCCGCTTTTGCCGTTGCTG‑CCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATc                       <  1:287781/151‑1 (MQ=255)                                                                                                                              ggAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACA‑GCCCTTCCGCTTTTGCCGTTGCTG‑CCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGc                <  2:595513/151‑1 (MQ=255)                                                                                                                                aaGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACA‑GCCCTTCCGCTTTTGCCGTTGCTG‑CCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCg              <  1:456585/151‑1 (MQ=255)                                                                                                                                 aGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACA‑GCCCTTCCGCTTTTGCCGTTGCTG‑CCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGa             <  2:116289/151‑1 (MQ=255)                                                                                                                                       tACCGGTCAGGGTAATCCACCGCGACCAGATACA‑GCCCTTCCGCTTTTGCCGTTGCTG‑CCGCCAGCGTTCTGTCCTTTGCCGCCCGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAatat       >  1:477099/1‑151 (MQ=255)                                                                                                                                            gTCAGGGTAATCCACCGCGACCAGATACA‑GCCCTTCCGCTTTTGCCGTTGCTG‑CCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTg  <  1:198489/151‑1 (MQ=255)                                                                                                                                            gTCAGGGTAATCCACCGCGACCAGATACA‑GCCCTTCCGCTTTTGCCGTTGCTG‑CCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTg  >  2:607114/1‑151 (MQ=255)                                                                                                                                                   |                                                                                                                                                  GTCCATATTTGCCTATGCCTTGTACTCGTCATCTTTCAGGCTGTAACTACGTTGGCTACAGCCTGAAATGTTCCGAGCATTATTCTCGTTAGTCCGCCAGAAATAGCGGGCCCATTGGCGGTTTTGGAAGATCATACCGGTCAGGGTAATCCACCGCGACCAGATACA‑GCCCTTCCGCTTTTGCCGTTGCTG‑CCGCCAGCGTTCTGTCCTTTGCCGCCAGCAACTCTGCTATCCAGCTCTCCGGCTGGTTGTGGGCACCGACTTCCATCAGGCTGCCGACAATATTCCTG  >  NC_000913/2434736‑2435025

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑